Your whole story is a bit confusing to me. When you say that you do as root
cp -rf /usr/SJL/* ./
then you copy to a relative path. Relative to the working directory. But as you do no not give any indication what the working directory (./) is, we can not goive any advice to the usefulness of this command.
Isn’t it far better to start from what you want instead of starting frrom some uncertain commands? You should find out what you want to make backups for. When you only want to cater for a user (you?) by incident destryoing/removing a file, then a backup to the same file system might be OK. When you want to be able to restore from a broken disk, you should of course backup to another physical disk (of course on a Linux file system). When you are afraid of a fire in the system, then you should use removeable mass storage and put that somewhere else in the house. When afraid of your house burned down, you should store the backup media elsewhere in town, etc.
Also, what to backup (some of this interacts with the above). When it is only about the data of one or more users, the user(s) could do that themselves. You could also, as a system manager, offer your users to do that for themm (as root). When you want to backup system data, like the configuration files in /etc, that should be done as root.
Etc. It is not obvious to design a backup policy.
So please first try to explain what you want to achieve. When that is to make a copy of a directory and all that is beneath it, to another directory and to keep that synchronised say every week (or other), then you should look into using rsync. It will only copy all files the first time it is called. After that it will only copy changed files and will delete removed files from the destination. And thus, normal, after the first copy is done, will only take a fraction of the time.
There are many possibilities. I, e.g., every week first make a copy of the existing backup in a way that I allways have the status of a maximum of 10 weeks. That means, that even after I made a backup and I need a file as it was three weeks ago, that is still possible. You could look into rsnapshot http://rsnapshot.org/. it is in the OSS repository. (It is script only, thus it is easy to get the basics out of it, it uses cp -al for making the generation copy and rsync for that backup itself, and program it yourself as I did, but you can of course also use as it is).
You story about different disks is a bit bewildering. You are not copying diks (or partitions) you are copying files. And for backups, it is of course better to copy them to a different file system, then to copy them on the same file system. (see above).